6-Plex Tandem Phosphorus Tags (TPT) for Accurate Quantitative Proteomics.

Isobaric chemical labeling is a widely used strategy for high-throughput quantitative proteomics based on mass spectrometry. However, commercially available reagents have high costs in applications as well as the sensitivity limitations for detection of the trace protein samples. Previously, we developed a 2-plex isobaric labeling strategy based on phosphorus chemistry for ultrasensitive proteome quantification with high accuracy. In this work, 6-plex tandem phosphorus tags (TPT) were developed with 3-fold increase in the multiplexing quantitative capacity compared to the 2-plex isobaric phosphorus reagents introduced previously. High isotope enrichment of 18O labeling was incorporated into the phosphoryl group with three exchangeable oxygen atoms by using commercially available H218O. The combinational incorporations of 18O atom in reporter ions and balance group set up the low-cost foundation for development of multiplex TPT reagents. The novel 6-plex TPT reagents could produce phosphoramidate as unique reporter ions with approximately 1 Da mass difference and thus enable 6-plex quantitative analysis in high-resolution ESI-MS/MS analysis. Using HeLa cell tryptic peptides, we concluded that 6-plex TPT reagents could facilitate large-scale accurate quantitative proteomics with very high labeling efficiency.

Regiochemical Analysis of the ProTide Activation Mechanism.

ProTides are nucleotide analogues used for the treatment of specific viral infections. These compounds consist of a masked nucleotide that undergoes in vivo enzymatic and spontaneous chemical transformations to generate a free mononucleotide that is ultimately transformed to the pharmaceutically active triphosphorylated drug. The three FDA approved ProTides are composed of a phosphoramidate (P-N) core coupled with a nucleoside analogue, phenol, and an l-alanyl carboxylate ester. The previously proposed mechanism of activation postulates the existence of an unstable 5-membered mixed anhydride cyclic intermediate formed from the direct attack of the carboxylate group of the l-alanyl moiety with expulsion of phenol. The mixed anhydride cyclic intermediate is further postulated to undergo spontaneous hydrolysis to form a linear l-alanyl phosphoramidate product. In the proposed mechanism of activation, the 5-membered mixed anhydride intermediate has been detected previously using mass spectrometry, but the specific site of nucleophilic attack by water (P-O versus C-O) has not been determined. To further interrogate the mechanism for hydrolysis of the putative 5-membered cyclic intermediate formed during ProTide activation, the reaction was conducted in 18O-labeled water using a ProTide analogue that could be activated by carboxypeptidase Y. Mass spectrometry and 31P NMR spectroscopy were used to demonstrate that the hydrolysis of the mixed anhydride 5-membered intermediate occurs with exclusive attack at the phosphorus center.

Rapid oxygen isotopic exchange between bicarbonate and water during photosynthesis.

Whether rapid oxygen isotopic exchange between bicarbonate and water occurs in photosynthesis is the key to determine the source of oxygen by classic 18O-labeled photosynthetic oxygen evolution experiments. Here we show that both Microcystis aeruginosa and Chlamydomonas reinhardtii utilize a significant proportion (>16%) of added bicarbonate as a carbon source for photosynthesis. However, oxygen isotopic signal in added bicarbonate cannot be traced in the oxygen in organic matter synthesized by these photosynthetic organisms. This contradicts the current photosynthesis theory, which states that photosynthetic oxygen evolution comes only from water, and oxygen in photosynthetic organic matter comes only from carbon dioxide. We conclude that the photosynthetic organisms undergo rapid exchange of oxygen isotope between bicarbonate and water during photosynthesis. At the same time, this study also provides isotopic evidence for a new mechanism that half of the oxygen in photosynthetic oxygen evolution comes from bicarbonate photolysis and half comes from water photolysis, which provides a new explanation for the bicarbonate effect, and suggests that the Kok-Joliot cycle of photosynthetic oxygen evolution, must be modified to include a molecule of bicarbonate in addition to one molecule of water which in turn must be incorporated into the cycle instead of two water molecules. Furthermore, this study provides a theoretical basis for constructing a newer artificial photosynthetic reactor coupling light reactions with the dark reactions.

Nuclear spin effects in biological processes.

Traditionally, nuclear spin is not considered to affect biological processes. Recently, this has changed as isotopic fractionation that deviates from classical mass dependence was reported both in vitro and in vivo. In these cases, the isotopic effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial dioxygen production system and biological aquaporin channels in cells. We observe that oxygen dynamics in chiral environments (in particular its transport) depend on nuclear spin, suggesting future applications for controlled isotope separation to be used, for instance, in NMR. To demonstrate the mechanism behind our findings, we formulate theoretical models based on a nuclear-spin-enhanced switch between electronic spin states. Accounting for the role of nuclear spin in biology can provide insights into the role of quantum effects in living systems and help inspire the development of future biotechnology solutions.

First Measurements on Triple Oxygen Isotopes of Dissolved Inorganic Phosphate in the Hydrosphere.

Although dissolved inorganic phosphate (DIP) is an important nutrient in the hydrosphere, it is difficult to quantitatively clarify the dynamics of DIP in the hydrosphere using the δ18O value of DIP as a tracer. In this study, we quantified the triple oxygen isotopic compositions (Δ'17O) of DIP relative to VSMOW with the reference line with a slope of 0.528 as an additional tracer to clarify the sources and dynamics of DIP in the hydrosphere. We found significant variation in the Δ'17O values of riverine DIP in urban areas, ranging from -107 × 10-6 to +3 × 10-6, while those of DIP in the effluents from wastewater treatment plants (WWTP) and DIP extracted from the chemical fertilizers showed -56 ± 5 × 10-6 (1SD) and -98 ± 5 × 10-6, respectively. We conclude that both the DIP supplied directly from the artificial loads (the WWTP effluent and chemical fertilizers) showing 17O-depleted Δ'17O values and the DIP turned over via the aquatic biosphere showing 17O-enriched Δ'17O values similar to ambient H2O were the major sources of riverine DIP. High-precision determination of the Δ'17O value of DIP can contribute to quantitative clarification of the dynamics of DIP in the hydrosphere.

High-Precision Triple Oxygen Isotope Analysis of Carbon Dioxide by Tunable Infrared Laser Absorption Spectroscopy.

Precision measurements of the stable isotope ratios of oxygen (18O/16O and 17O/16O) in CO2 are critical to atmospheric monitoring and terrestrial climate research. High-precision 17O measurements by isotope ratio mass spectrometry (IRMS) are challenging because they require complicated sample preparation procedures, long measurement times, and relatively large samples sizes. Recently, tunable infrared laser direct absorption spectroscopy (TILDAS) has shown significant potential as an alternative technique for triple oxygen isotope analysis of CO2, although the ultimate level of reproducibility is unknown, partly because it is unclear how to relate TILDAS measurements to an internationally accepted isotope abundance scale (e.g., VSMOW2-SLAP2). Here, we present a method for high-precision triple oxygen isotope analysis of CO2 by TILDAS, requiring ∼8-9 µmol of CO2 (or 0.9 mg carbonate) in 50 min, plus ∼1.5 h for sample preparation and dilution of CO2 in N2 to a nominal 400 µmol mol-1. Overall reproducibility of Δ'17O (CO2) was 0.004‰ (4 per meg) for IAEA603 (SE, n = 6) and 10 per meg for NBS18 (SE, n = 4). Values corrected to the VSMOW2-SLAP2 scale are in good agreement with established techniques of high-precision IRMS, with the exception of Δ'17O measured by platinum-catalyzed exchange of CO2 with O2. Compared to high-precision IRMS, TILDAS offers the advantage of ∼10 times less sample, and greater throughput, without loss of reproducibility. The flexibility of the technique should allow for many important applications to global biogeochemical monitoring and investigation of 17O anomalies in a range of geological materials.

Water-solid contact electrification causes hydrogen peroxide production from hydroxyl radical recombination in sprayed microdroplets.

Contact electrification between water and a solid surface is crucial for physicochemical processes at water-solid interfaces. However, the nature of the involved processes remains poorly understood, especially in the initial stage of the interface formation. Here we report that H2O2 is spontaneously produced from the hydroxyl groups on the solid surface when contact occurred. The density of hydroxyl groups affects the H2O2 yield. The participation of hydroxyl groups in H2O2 generation is confirmed by mass spectrometric detection of 18O in the product of the reaction between 4-carboxyphenylboronic acid and 18O-labeled H2O2 resulting from 18O2 plasma treatment of the surface. We propose a model for H2O2 generation based on recombination of the hydroxyl radicals produced from the surface hydroxyl groups in the water-solid contact process. Our observations show that the spontaneous generation of H2O2 is universal on the surfaces of soil and atmospheric fine particles in a humid environment.

Accurate and Efficient SIMS Oxygen Isotope Analysis of Composition-Variable Minerals: Online Matrix Effect Calibration for Dolomite.

High-quality oxygen isotope analysis of composition-variable minerals (e.g., ubiquitous carbonates) using secondary ion mass spectrometry (SIMS) is extremely challenging. The classical off-line procedure, which requires additional electron probe microanalyzer (EPMA) chemical compositions for calibrating instrumental mass fractionation (IMF), is inherently inaccurate and analytically inefficient. In this study, the first accurate and paired SIMS analysis of δ18O and Fe# [molar Fe/(Mg + Fe)] in dolomite is reported. Based on five newly developed dolomite O-isotopic standards with an Fe# range of 0.01-0.35 obtained by SIMS, a novel accurate and rapid online matrix effect calibration method for dolomite O-isotope analysis was developed using concurrent SIMS 18O-16O-56Fe16O-24Mg16O measurements without additional chemical electron probe microanalysis. A logistic equation was proposed as the best-fit curve to represent the δ18O matrix effect based on the 56Fe16O/24Mg16O ratios. For CTD-4 carbonatitic dolomite with variable Fe# but homogeneous oxygen isotopes, the off-line method exhibited highly variable apparent δ18O values in the range of 5.74-10.11‰. The online method yielded a homogeneous δ18O value of 7.94 ± 0.34‰ (2SD, n = 40), which is comparable with that of bulk analysis (7.94 ± 0.20‰; 2SD). Comprehensive analyses validated the online method as the best strategy for performing accurate δ18O analysis of samples with highly heterogeneous compositions. Based on its accuracy, simplicity, and economic feasibility, this method has potential applications in the analysis of composition-complex dolomites, detrital dolomites, and other precious terrestrial and extraterrestrial materials.

Rapid, Quantitative Nuclear Magnetic Resonance Test for Oxygen-17 Enrichment in Water.

Nuclear magnetic resonance (NMR) studies involving 17O are increasingly important in molecular biology, material science, and other disciplines. A large number of these studies employ H217O as a source of 17O, and this reliance can be limiting because the high cost of H217O. To overcome this constraint, a recent study proposed a distillation scheme capable of producing significant quantities of H217O at a low cost. Although this method is reported to be effective, the reactions proposed to quantify percent of 17O enrichment are either time intensive or have a risk of errors due to the isotope effect. Here, an alternative reaction scheme is described to measure 17O water that ultimately creates methyl benzoate as the sole 17O-containing product. The proposed reaction is completed in a matter of minutes at room temperature, produces only one 17O product, and requires no clean-up step. The large isotope shift observed in solution NMR between the 13C═16O and 13C═17O resonances allows for integration of the individual peaks. This 13C NMR analysis is found to be highly accurate over a wide enrichment range and is accessible to most NMR spectroscopists.

Fast and pervasive diagenetic isotope exchange in foraminifera tests is species-dependent.

Oxygen isotope compositions of fossil foraminifera tests are commonly used proxies for ocean paleotemperatures, with reconstructions spanning the last 112 million years. However, the isotopic composition of these calcitic tests can be substantially altered during diagenesis without discernible textural changes. Here, we investigate fluid-mediated isotopic exchange in pristine tests of three modern benthic foraminifera species (Ammonia sp., Haynesina germanica, and Amphistegina lessonii) following immersion into an 18O-enriched artificial seawater at 90 °C for hours to days. Reacted tests remain texturally pristine but their bulk oxygen isotope compositions reveal rapid and species-dependent isotopic exchange with the water. NanoSIMS imaging reveals the 3-dimensional intra-test distributions of 18O-enrichment that correlates with test ultra-structure and associated organic matter. Image analysis is used to quantify species level differences in test ultrastructure, which explains the observed species-dependent rates of isotopic exchange. Consequently, even tests considered texturally pristine for paleo-climatic reconstruction purposes may have experienced substantial isotopic exchange; critical paleo-temperature record re-examination is warranted.

Two- and Three-Dimensional 13C-17O Heteronuclear Correlation NMR Spectroscopy for Studying Organic and Biological Solids.

We report two- and three-dimensional (2D and 3D) 13C-17O heteronuclear correlation solid-state NMR experiments under magic-angle spinning (MAS) conditions. These experiments utilize the D-RINEPT (Dipolar-mediated Refocused Insensitive Nuclei Enhanced by Polarization Transfer) scheme with symmetry-based SR412 recoupling blocks for coherence transfer between 13C and 17O nuclei. First, a 2D 17O → 13C correlation experiment was performed for the [1-13C,17O]-Gly/Gly·HCl cocrystal and [U-13C, 1-17O]-α/ß-d-glucose samples. Second, a 2D 17O → 13C MQ-D-RINEPT correlation experiment where the indirect dimension incorporates the multiple-quantum MAS (MQMAS) scheme was tested for obtaining isotropic 17O resolution with [U-13C, 1-17O]-α/ß-d-glucose. Third, a new 3D 17O → 13C → 13C correlation experiment was demonstrated where 17O → 13C and 13C → 13C correlations are achieved by D-RINEPT and DARR (Dipolar Assisted Rotational Resonance) sequences, respectively (thus termed as a 3D D-RINEPT/DARR OCC experiment). This new 3D 17O NMR experiment is implemented with the aim for site-resolved solid-state 17O NMR studies.

Comparison of isotope ratio mass spectrometry and cavity ring-down spectroscopy procedures and precision of the doubly labeled water method in different physiological specimens.

RATIONALE: This study determines if saliva collection procedures for the doubly labeled water (DLW) method, used for measuring total energy expenditure (TEE), are comparable to urine and plasma collection. Both the cavity ring-down spectroscopy (CRDS) and isotope ratio mass spectrometry (IRMS) analyses techniques are compared. METHODS: Saliva specimens were collected from participants for the DLW method. The specimens were collected under different conditions: after consumption of tap water, after chewing gum, and during exposure to conditions of high and low relative humidity. The isotopes in saliva were compared with simultaneous plasma and urine collection. TEE calculated from saliva and analyzed using CRDS was compared to that of plasma analyzed using IRMS. RESULTS: The within-individual variances were not significantly different between the saliva specimens (0.4‰) and plasma (0.3‰). After the oral dose of DLW, the saliva specimens displayed a shorter equilibration time to urine. When participants consumed 500 mL of tap water, the enrichment of saliva specimens reached a new plateau value faster than urine. Saliva collection exposed to high ambient humidity conditions was slightly less enriched as compared to low-humidity conditions while urine enrichment was unaffected. In contrast, whereas the within-individual effects of gum chewing during saliva collection on 18 O were unaffected, the abundance of 2 H in saliva was slightly lower after chewing the gum. The within-individual difference between TEE calculated from saliva and that calculated from plasma analyzed using IRMS did not differ from zero, and the standard deviation was not different from that predicted by a propagation of error analysis based on analytical error alone. CONCLUSIONS: Our findings support using saliva specimens for the DLW method. The analysis of plasma and urine, however, requires reducing the memory effect resulting from contaminants. Also, it should be performed in a manner that minimizes exposure to air where specimens may be exposed to evaporation or contamination from water vapor during sampling.

18 O/16 O-Encoding Strategy for Microscale Stereochemical Determination of Peptidic Natural Products.

The demand for more efficient methods of establishing the undetermined stereochemistries of peptidic natural products continues unabated. A new method for microscale stereochemical determination was devised by integrating solid-phase synthesis, split-and-mix randomization, 18 O/16 O-encoding of d/l-configurations, tandem mass spectrometry, and biological evaluation. Here we applied gramicidin A as the molecule for a blind test. Gramicidin A and its 31 diastereomers were randomly prepared in microgram scale with 18 O/16 O-stereochemical encoding and subjected to MS/MS-structural determination and cytotoxicity assay. Only the parent gramicidin A was selected from among the 32 stereoisomers, validating the high reliability of the present strategy.

Isolation of a Ru(IV) side-on peroxo intermediate in the water oxidation reaction.

The electrons that nature uses to reduce CO2 during photosynthesis come from water oxidation at the oxygen-evolving complex of photosystem II. Molecular catalysts have served as models to understand its mechanism, in particular the O-O bond-forming reaction, which is still not fully understood. Here we report a Ru(IV) side-on peroxo complex that serves as a 'missing link' for the species that form after the rate-determining O-O bond-forming step. The Ru(IV) side-on peroxo complex (η2-1iv-OO) is generated from the isolated Ru(IV) oxo complex (1iv=O) in the presence of an excess of oxidant. The oxidation (IV) and spin state (singlet) of η2-1iv-OO were determined by a combination of experimental and theoretical studies. 18O- and 2H-labelling studies evidence the direct evolution of O2 through the nucleophilic attack of a H2O molecule on the highly electrophilic metal-oxo species via the formation of η2-1iv-OO. These studies demonstrate water nucleophilic attack as a viable mechanism for O-O bond formation, as previously proposed based on indirect evidence.

Cost-efficient and user-friendly 17O/18O labeling procedures of fatty acids using mechanochemistry.

Two mechanochemical procedures for 17O/18O-isotope labeling of fatty acids are reported: a carboxylic acid activation/hydrolysis approach and a saponification approach. The latter route allowed first-time enrichment of important polyunsaturated fatty acids (PUFAs) including docosahexaenoic acid (DHA). Overall, a total of 9 pure labeled products were isolated in high yields (≥80%) and with high enrichment levels (≥37% average labeling of C=O and C-OH carboxylic oxygen atoms), under mild conditions, and in short time (

What's in a wine? - A spot check of the integrity of European wine sold in China based on anthocyanin composition, stable isotope and glycerol impurity analysis.

The international wine market has been repeatedly hit by cases of fraud in recent decades. While several studies attested a special vulnerability of the fast growing wine business in China, reports on chemical analyses of commercial wine samples are rare. We examined 50 predominantly red wines with European labelling, which were purchased on the Chinese market, for fraud-relevant parameters. More than 20% of the tested samples revealed anomalies in relation to the stable isotope ratios of D/H, 18O/16O and 13C/12C, contents of technical glycerol by-products or anthocyanin composition. These results strongly suggested watering of the wines, chaptalisation, glycerol addition or the use of non-Vitis anthocyanin sources, respectively. Some of these samples also showed suspicious spelling errors or other irregularities in the labelling, but the majority appeared genuine to the eye. Hence, this spot check demonstrates the importance of chemical authenticity analysis of market samples in order to detect fraudulent products. Moreover, we used the same sample set for an evaluation of the Chinese standard method for carbon stable isotope determination of wine ethanol in comparison to the current OIV (International Organisation of Vine and Wine) standard method. The results of a Bland-Altman analysis indicated that the methods can be applied interchangeably. As the two methods differ in their workflow and in the requested equipment, this might eventually enable more laboratories to perform 13C/12C analysis of wine and spirits.

Direct imaging of glymphatic transport using H217O MRI.

The recently proposed glymphatic pathway for solute transport and waste clearance from the brain has been the focus of intense debate. By exploiting an isotopically enriched MRI tracer, H217O, we directly imaged glymphatic water transport in the rat brain in vivo. Our results reveal glymphatic transport that is dramatically faster and more extensive than previously thought and unlikely to be explained by diffusion alone. Moreover, we confirm the critical role of aquaporin-4 channels in glymphatic transport.

Identification of ß-carotene oxidation products produced by bleaching clay using UPLC-ESI-MS/MS.

The removal of plant pigments such as ß-carotene is an aspect of vegetable oil processing often desired by the food and pharmaceutical industries. Adsorption of ß-carotene to acid-activated clay (AAC) is a well-established method for purification. Despite this, the removal mechanism of ß-carotene is not well understood. UPLC-MS/MS analysis of surface compounds extracted from ß-carotene-AAC (BC-AAC) complexes show that AAC acts as an oxidiser. Oxidation products detected included canthaxanthin and 3',4'-didehydro-ß-caroten-4-one. AAC had surface water exchanged with an 18O labelled water and was then exposed to ß-carotene. Carotenoids labelled with 18O were produced from this reaction, suggesting surface water is necessary for ß-carotene removal.

Four Isotope-Labeled Recombination Pathways of Ozone Formation.

A theoretical approach is developed for the description of all possible recombination pathways in the ozone forming reaction, without neglecting any process a priori, and without decoupling the individual pathways one from another. These pathways become physically distinct when a rare isotope of oxygen is introduced, such as 18O, which represents a sensitive probe of the ozone forming reaction. Each isotopologue of O3 contains two types of physically distinct entrance channels and two types of physically distinct product wells, creating four recombination pathways. Calculations are done for singly and doubly substituted isotopologues of ozone, eight rate coefficients total. Two pathways for the formation of asymmetric ozone isotopomer exhibit rather different rate coefficients, indicating large isotope effect driven by ΔZPE-difference. Rate coefficient for the formation of symmetric isotopomer of ozone (third pathway) is found to be in between of those two, while the rate of insertion pathway is smaller by two orders of magnitude. These trends are in good agreement with experiments, for both singly and doubly substituted ozone. The total formation rates for asymmetric isotopomers are found to be somewhat larger than those for symmetric isotopomers, but not as much as in the experiment. Overall, the distribution of lifetimes is found to be very similar for the metastable states in symmetric and asymmetric ozone isotopomers.

The Structural and Biochemical Basis of Apocarotenoid Processing by ß-Carotene Oxygenase-2.

In mammals, carotenoids are converted by two carotenoid cleavage oxygenases into apocarotenoids, including vitamin A. Although knowledge about ß-carotene oxygenase-1 (BCO1) and vitamin A metabolism has tremendously increased, the function of ß-carotene oxygenase-2 (BCO2) remains less well-defined. We here studied the role of BCO2 in the metabolism of long chain ß-apocarotenoids, which recently emerged as putative regulatory molecules in mammalian biology. We showed that recombinant murine BCO2 converted the alcohol, aldehyde, and carboxylic acid of a ß-apocarotenoid substrate by oxidative cleavage at position C9,C10 into a ß-ionone and a diapocarotenoid product. Chain length variation (C20 to C40) and ionone ring site modifications of the apocarotenoid substrate did not impede catalytic activity or alter the regioselectivity of the double bond cleavage by BCO2. Isotope labeling experiments revealed that the double bond cleavage of an apocarotenoid followed a dioxygenase reaction mechanism. Structural modeling and site directed mutagenesis identified amino acid residues in the substrate tunnel of BCO2 that are critical for apocarotenoid binding and catalytic processing. Mice deficient for BCO2 accumulated apocarotenoids in their livers, indicating that the enzyme engages in apocarotenoid metabolism. Together, our study provides novel structural and functional insights into BCO2 catalysis and establishes the enzyme as a key component of apocarotenoid homeostasis in mice.